The bottom of Chesapeake Bay is a battleground littered with the empty shells of dead oysters. Gone, for the most part, are the living oyster reefs that once created habitat for small fish and crabs and helped filter Bay waters now cloudy with excess plankton.

Tongers and dredgers and police once fought over those reefs in the infamous centuries. But today the combatants include watermen and oyster growers, scientists and state agencies and environmental organizations. And the core battles rage not over how to harvest the reefs, but how best to rebuild them. Should we replant the Bay with native oysters — or with non-natives imported from China?

The answer may depend in part on another question: what killed off the oyster reefs of the Chesapeake in the first place? The suspects include disease, overfishing, sedimentation, habitat destruction, and water quality changes. Of all the well-known oyster killers, the most dramatic in recent decades was MSX, an epidemic that began in the late 1950s. An unknown parasite, MSX was a terrible swift sword, slashing harvests by 90 percent on the oyster grounds of Delaware Bay and by 75 percent in the Virginia Chesapeake in its first three years. The result was disaster: an oyster-killing disease that altered the ecology of two estuaries and nearly wiped out oyster industries in three states.

Where did this killer parasite come from? When Gene Burreson and Nancy Stokes of the Virginia Institute of Marine Science found a way to solve this long-standing mystery, their findings represented a landmark in the annals of Chesapeake Bay science, but a landmark that was a long time coming. Although scientists first began investigating the origins of MSX in 1958, the 20th century would come to an end before Burreson and Stokes could eventually publish their findings. In the year 2000, they finally identified this deadly parasite as a foreign invader.

Why did it take more than 40 years to answer such a key question? Faced with a parasite of unknown origins, marine biologists in the 1950s and 1960s found themselves working at the limits of their current tool set, waiting for a breakthrough. In the history of science, when new research tools come online, new discoveries soon follow — after new telescopes start up, new galaxies appear in the depths of space; after deep submersibles plunge to the sea floor, hydrothermal vents appear in the depths of the world's oceans.

For Burreson and Stokes and biologists everywhere, the invention of a new tool called PCR — short for polymerase chain reaction — created a revolution in their science in the early 1990s. Using the new DNA-based tools of molecular biology, Burreson and Stokes were at last able to trace the origins of the MSX epidemic to a parasite that invaded from elsewhere, probably as a hitchhiker on a non-native oyster.

If there are lessons to be learned from that long history, one of them might be this: breakthroughs can breed hubris, what physicist Freeman Dyson called "a technical arrogance that overcomes people when they see what they can do with their minds." Innovations like PCR and novel technologies for oyster aquaculture open up discoveries and expand the options for commercial and ecological restoration, reviving a dream in the oyster industry of planting the Chesapeake with faster-growing non-natives.

That dream focuses now on a Chinese oyster called Crassostrea ariakensis, but the vision has been around for 60 years, spurred by the commercial success of Japanese oyster aquaculture in the Pacific Northwest. If it could be done elsewhere, the thinking goes, it could be tried here also.

Humility, however, might be another lesson from history, humility in the face of the unknown and the untried. The devastation of MSX dates back 50 years now, and 40 of these years passed before scientists, thanks to a breakthrough, finally solved the puzzle of its unknown origins.

Ironically enough, the scientists responsible for breakthroughs often see — more clearly than most — the limits of their knowledge. Some researchers warn that we'll never have enough knowledge ahead of time to predict accurately the outcome of widespread introductions. If we want to know the answer, we have to run the experiment.

The restoration of Chesapeake oysters will be exactly that: a huge, system-wide experiment in the country's largest estuary. And the outcome is unknowable.